American Mineralogist, Volume 88, pages 247–250, 2003
The American Mineralogist crystal structure database
ROBERT T. DOWNS* AND MICHELLE HALL-WALLACE
Department of Geosciences, University of Arizona, Tucson, Arizona 85721-0077, U.S.A.
ABSTRACT
A database has been constructed that contains all the crystal structures previously published in
the American Mineralogist. The database is called “The American Mineralogist Crystal Structure
Database” and is freely accessible from the websites of the Mineralogical Society of America at
http://www.minsocam.org/MSA/Crystal_Database.html and the University of Arizona. In addition
to the database, a suite of interactive software is provided that can be used to view and manipulate
the crystal structures and compute different properties of a crystal such as geometry, diffraction
patterns, and procrystal electron densities. The database is set up so that the data can be easily
incorporated into other software packages. Included at the website is an evolving set of guides to
instruct the user and help with classroom education.
INTRODUCTION
The structure of a crystal represents a minimum energy configuration adopted by a collection of atoms at a given temperature and pressure. In principle, all the physical and chemical
properties of any crystalline substance can be computed from
knowledge of its crystal structure. The determination of crystal structures and the deduction and understanding of these
computational algorithms constitutes a major part of scientific
research in physics, chemistry, biology, medicine, mineralogy,
geology, and material sciences. As such, crystal structure data
represent one of the most important resources for developing
our scientific knowledge and thus should be archived in ways
that make them easy to access and preserve. However, this data
is often cumbersome to retrieve and verify from the literature
and even more difficult to analyze for many scientists for whom
crystallography is not their primary discipline. Thus, the Mineralogical Society of America and the University of Arizona
have established a collection of mineralogically important crystallographic data sets that are freely accessible through the
Internet. This database is an important resource to the Mineralogical Society of America and the Society is committed to
maintain it as part of its outreach program (Alex Speer, the
Executive Director of MSA, personal communication).
THE DATABASE
The database contains every experimentally determined
crystal structure reported in the American Mineralogist. Including the data published through the end of the 2001 calendar
year, we have collected 2627 individual data sets representing
1007 unique mineral and chemical species. The data represent
structures determined at ambient conditions as well as at temperature or pressure. Constructing the database is a multi-step
process that includes: (1) examining each volume of the American Mineralogist to identify all papers that report crystal structures; (2) manually entering the reported data in the database;
(3) verifying the consistency of the data with reported crystal
chemical parameters; (4) contacting the authors about
irresolvable inconsistencies between reported and computed
FIGURE 1. An example of the crystallographic data included in the
database.
* E-mail: downs@geo.arizona.edu
0003-004X/03/0001–247$05.00
parameters; (5) incorporating comments from either the original authors or ourselves when changes are made to the originally published data. Each record in the database consists of a
bibliographic reference, cell parameters, symmetry, atomic
positions, displacement parameters, and site occupancies. An
example of a data set is provided in Figure 1.
The first part of each data set contains identifying information, bibliography and notes, while the second part contains
the crystallographic parameters. The first line of a data file
contains an identifier, such as the name of the mineral or formula of the chemical species. The next line(s) contain the names
of the authors, each separated by a comma. This is followed by
the journal reference, title of the paper, and additional notes.
The crystallographic data begins with a listing of the cell parameters and space group. If the data is given with respect to a
non-standard space group origin then an asterisk precedes the
space group symbol and the next line contains the translation
vector from the standard origin. The 1952 edition of the International Tables for X-ray Crystallography are used to define
the standard origin. The rest of the data set is a fixed-formatted
listing of the atoms, their positional and displacement parameters, and occupancies. A header is provided that defines rightjustified columns. The name of each atom identifies the
occupying elements, with additional identifiers added when
appropriate. For instance, “Oco” identifies a particular oxygen
atom in the albite structure. Some data sets report a crystallographic site occupied by molecular species rather than elemental, such as OH, water or methane. In most of these cases the
atom name is denoted by molecular formula. For example,
“CH4” denotes methane, and “Wat” denotes water. The displacement factors are tabulated in one of two formats, U’s or b’s
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DOWNS AND HALL-WALLACE: THE AMERICAN MINERALOGIST CRYSTAL STRUCTURE DATABASE
(see Downs 2000 for further details on displacement factors).
Quality control is an area of major concern and effort in
construction of the database. Each data set must be verified for
accuracy and omissions before being added to the database.
We use METRIC, a software program developed by Bartelmehs,
Gibbs, Boisen, and Downs (1993) at Virginia Tech. This program was written using the matrix methods and group theory
outlined in Boisen and Gibbs (1990) to compute the crystal
chemical parameters that are typically found in many crystal
structure publications. The crystal chemical parameters include
bond lengths, angles, polyhedral volumes, distortion indices,
displacement parameter details, rigid-body motion parameters,
and such, as recently reviewed in Hazen et al. (2000). The software has been widely used for crystal structure research and
educational purposes (Bartelmehs et al. 1993). Comparing the
crystal chemical parameters calculated by METRIC with those
included in the original publication provides a check of the
internal consistency of the data. If a discrepancy is found then
we try to determine its source and correct it. Many errors are
typographical, while others are more complex. The authors are
contacted to correct an error when possible. The database contains only the corrected data set. The METRIC software that
we use to check the data is freely available and is distributed
on the website.
Our experience has shown that the number of publications
with errors in their data is large. We estimate that at least 50%
of the published data have errors of one sort or another that
require deducing the problem and contacting the authors. To
address this problem, the American Mineralogist has appointed
a crystal structure technical editor (currently R.T. Downs). The
editor checks the internal consistency of the data for each structure that is being reported in a submitted manuscript using the
METRIC software. The results of the check are forwarded to
both the primary editor and the authors so that the manuscript
can be corrected before publication. We estimate that 75% of
all submitted manuscripts have errors of one sort or another in
their crystallographic tables. Anne Hofmeister, recent editor of
American Mineralogist, and Robert Martin, editor of the Canadian Mineralogist, can corroborate this high percentage of
errors (personal communications).
THE ANCILLARY SOFTWARE
A suite of software visualization and analysis tools has been
developed to make the database more useful as a scientific and
educational tool. Two key applications are XtalDraw, an application that creates multiple representations of a crystal structure, and METRIC, described above.
The XtalDraw and METRIC modules, with their options
and interface, are the result of many years of development. The
software was written for DOS systems in 1986 at Virginia Tech
(Bartelmehs et al. 1993) for two purposes: (1) to aid teaching
in the Geosciences, Material Sciences, and Mathematics programs at the university, and (2) to facilitate research. These
goals have been maintained over the years. Through interaction with undergraduates who use the software in class, the
interface algorithms have been streamlined to be simpler and
more intuitive, however, these refinements serve the professional scientist as well.
While powerful, they still are not completely user-friendly
and may often require significant experience or oversight by
an instructor to use them in a classroom setting. Furthermore,
the applications are not fully compatible with the crystal structure database nor do they provide for seamless data analysis.
With a grant from the National Science Foundation, we are
working to transform these powerful applications into a more
user-friendly visualization and analysis tool set, fully integrated
with the crystal structure database. This will make the database more useful and accessible. Below we describe the existing software and provide insight into how it will evolve.
When completed, students and scientists of all disciplines
will be able to explore and analyze crystal structure data with a
state-of-the-art Windows-based software. The basic features of
the software will include default settings that allow a range of
users, from the high school student in chemistry to the professional mineralogist, to investigate fundamental properties of
minerals including: (1) crystal chemical parameters such as bond
lengths and angles, polyhedral volumes and distortions, thermal
vibration amplitudes, and rigid body motion parameters; (2) fixed
wavelength or energy dispersive X-ray and neutron powder diffraction patterns; and (3) electron densities and bonding analyses.
Crystallographic parameters are the foundation of research
in material properties and being able to visualize and manipulate crystal structures is fundamental to understanding them.
Thus, when a crystal structure in the database is accessed, it
can automatically be displayed with the XtalDraw module
(Bartelmehs et al. 1993; Downs and Bartelmehs 1996; Hazen
and Downs 1996; Downs 1998; Hazen et al. 2000). Currently,
this stand-alone software contains options to draw the crystal
structure with ball and stick, polyhedral, and thermal ellipsoidal renderings (Fig. 2). The user can rotate the image with the
arrow keys, or manually enter directions of view in direct or
reciprocal space coordinates. They can expand or shrink the
image, and add or delete atoms from the field of view. The
number of displayed atoms will depend only upon available
computer memory. Users can change the colors of atoms, their
sizes, the bonds, and so forth. The software produces publication quality bitmaps of any desired size. Carefully selected
default viewing parameters are one very powerful feature of
XtalDraw that make it easy to use. For instance, after a data
file is read, the structure is initially displayed with c* coming
out of the screen, in a default orientation established by the
International Tables for Crystallography. The atoms are drawn
in a set of colors suggested by Lipson and Cochran (1957) to represent elemental species, and in sizes that scale to the Shannon
and Prewitt (1969) radii. The user has the option to change these
settings at any time and to establish their own default settings. The
software can also be used to make animations of crystal structures
that change with temperature, pressures, or composition (Downs
and Heese 2000).
The database software module also integrates the ability to calculate many of the important crystal chemical parameters that are
used by today’s researchers, such as bond lengths and angles, polyhedral volumes and distortion parameters, vibrational amplitudes
and orientations (Hazen et al. 2000) using the METRIC module.
Another important property of a crystal that can be computed from its structural data is its diffraction pattern. Neutron
DOWNS AND HALL-WALLACE: THE AMERICAN MINERALOGIST CRYSTAL STRUCTURE DATABASE
FIGURE 2. An example of interactive displays that can be created by
the software associated with the American Mineralogist Crystal Structure
Database. The example includes images of (a) the crystal structure of
jadeite in a combined polyhedral and ellipsoidal rendering made with
XtalDraw; (b) the powder diffraction pattern of jadeite using MoKa
radiation made with XPOW; and (c) an electron density map of the plane
through Na and bridging O atoms in jadeite made with SPEEDEN.
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and X-ray powder diffraction patterns, generated from a fixed
source or from an energy dispersive source, such as at a synchrotron, can be computed with the software XPOW (Downs
et al. 1993). Currently, XPOW calculates the diffraction pattern for any crystalline substance and provides an interactive
display of the pattern, as it would be generated by a conventional powder diffractometer (Fig. 2). The user can alter the
radiation source wavelength, the peak widths, limits and orientation of the display. It provides a way to learn about the
relationship between a crystal structure and a diffraction pattern by allowing the user to adjust parameters and view the
changes. It is also of great use in identifying unknown materials by providing a complete diffraction pattern, and not just the
few d-spacings listed in a search-match table.
SPEEDEN, a program that can produce a standardized electron density distribution for a given crystal structure, will also
be integrated in the software package. The electron density is
generally very difficult and time-consuming to obtain from
experiment, and expensive and time consuming to compute.
However, the procrystal model (also known as the independent
atom model, IAM) of the electron density is surprisingly simple to
obtain (Gibbs et al. 1992). Functions for spherically averaged electron densities are placed at the observed positions of the atoms in
a crystal and the electron density for the crystal is computed by the
superposition principle. This model provides a quite accurate description of the true electron density, especially around the heavier
atoms (Coppens 1997; Downs et al. 2002).
Recent work pioneered by Bader (1995) and co-workers
provides algorithms for analysis of the topology of the electron density. In particular, a pair of atoms is bonded if and only
if a ridge of electron density joins the pair and there is a saddle
point at the minimum between the atoms. Thus, for the first
time, we have an unambiguous way to determine if two atoms
are bonded. Downs et al. (2002) shows that the procrystal model
provides a determination of bonding that is consistent with that
produced by full quantum calculations for a large number of
inorganic structures. The analysis and use of electron density
to determine bonding is still a new tool in the mineralogical
community (Downs et al. 1996; Downs et al. 1999; Gibbs et al.
1992, 1998; Rakovan et al. 1999) and so this software will be
of great use to researchers. The SPEEDEN (SPhErically averaged Electron DENsity program) module was originally coded
by two high-school students, Andalman and Hudasko, who won
the First Place Grand Award at the 1995 International Science
and Engineering Fair with this project (Andalman et al. 1995;
Downs et al. 1996). Figure 2 shows a contour map of the electron density in a part of the structure of jadeite. This image was
generated by computing a grid of electron density data with
SPEEDEN, and then importing the grid into commercial contouring software.
As this project progresses, additional software will be developed and made accessible from the database website. We
invite other researchers to also contribute their software and
forward suggestions for improving our existing software.
ACCESSING THE DATABASE INFORMATION
A good database should be comprehensive, accurate, easily
accessed, and easily analyzed. When completed, the Crystal
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DOWNS AND HALL-WALLACE: THE AMERICAN MINERALOGIST CRYSTAL STRUCTURE DATABASE
Structure database will meet all of these criteria. Currently,
access is provided through a search procedure that consists of
drop-down list boxes containing the names of the minerals or
chemical species, the authors and titles of the relevant journal
articles, as well as fields for chemistry, unit-cell dimensions,
and space group symmetry. There is also a field to enter a general search for words or phrases. These fields can be combined
with the logical conditions or and and in a search.
The search algorithm uses MYSQL with the following
scheme. Each data set is stored as a separate file, identified by
volume number and page number of the reference with the file
extension *.amc. Associated with each filename are entries in
the database that correspond to mineral name, authors, title,
chemical elements present in the data set, cell parameters, and
space group. The website interface is constructed dynamically
using php programming.
After the search criteria are defined and the search is initialized, the php program collates the contents of the pertinent data
files and displays them on a new screen. The user has several options. They can cut-and-paste the relevant text, or select an individual data set, or select the entire set of data. Since the data files
are stored on an ftp server, the user can then download the selected
files to their own computer through an ftp hyperlink. If the file
extension of the data, *.amc, has been associated with an application on the user’s local computer, then the application will be
launched and should automatically open the file. For instance,
XtalDraw can be launched in this manner, so that choosing a data
set of the website opens up an interactive drawing of the crystal
structure on a PC. This feature is modeled after the *.pdf interface
with Adobe Acrobat Reader.
In addition to accessing data through the web-based interface
described above, a search can be initialized from any web page by
sending a php query to the website. A successful search would
bring up the data without going through our search interface. This
method for accessing the data is currently being used by databases
such as http://www.webmineral.com and would be a good way to
provide access to the data through education web pages. The details for constructing this type of search can be found at the website.
THE EDUCATIONAL COMPONENT
Our current database provides fast and easy access to crystal
structure data in a tabular format. In its current form, this data is
most useful to the professional mineralogist who has a good understanding of crystallography or for those in an educational setting where some training may be provided. Implementing the
software enhancements will greatly improve the ease of use and
create a seamless interface between the data and each software
module. This will open the door to a much wider audience of users. To complete the outreach goals of the database, a set of instructional modules or guides are being developed to provide
tutorials that explain how to use the software, as well as an exploration of the data and fundamental properties of crystals. In
particular, guides will be designed for: (1) analysis of the structural systematics of pyroxenes as a means to learn how to use
the XtalDraw module; (2) analysis of the behavior of pyroxenes
as a function of temperature as a means to learn how to make
animations (Downs and Heese 2000); (3) investigation of the
relationship between crystal structure and diffraction pattern
as a way to learn how to use the XPOW diffraction module; (4)
analysis of the bonding changes displayed by the pyroxene
structure as it transforms from one symmetry to another, as a
means to learn how to use the electron density module,
SPEEDEN.
These guides will be also be turned into complete lesson
plans so that high school teachers and university faculty can
use them to introduce students to the software. The lesson plans
will be tested in the classroom in the natural course of teaching
mineralogy at the University of Arizona prior to publication.
REFERENCES CITED
Andalman, A., Hudasko, M., and Downs, R.T. (1995) An electron density study of the
bonding of Na and Oco in low albite. EOS Transactions, AGU, Spring Meeting
Supplement, 76, 154.
Bader, R.F.W. (1995) Atoms in molecules, a quantum theory, 438 p. Oxford University
Press, New York,
Bartelmehs, K.L., Gibbs, G.V., Boisen, M.B. Jr., and Downs, R.T. (1993) Interactive
computer software used in teaching and research in mineralogy at Virginia Tech.
Geological Society of America Fall Meeting, Boston, A-347.
Boisen, M.B. Jr. and Gibbs, G.V. (1990) Mathematical Crystallography, Volume 15 Revised. Reviews in Mineralogy, Mineralogical Society of America, Washington D.C.
Coppens, P. (1997) X-ray charge densities and chemical bonding, 358 p. International
Union of Crystallography, Oxford University Press, New York.
Downs, R.T. (1998) Computer graphics simulation of compression mechanisms in crystals. IUCR-HP98, Argonne, Illinois, Abstracts, 21.
———(2000) Analysis of harmonic displacement factors. Reviews in Mineralogy and
Geochemistry, 41, High-Temperature and High-Pressure Crystal Chemistry, Robert
M. Hazen and Robert T. Downs, Editors. Mineralogical Society of America, Washington D.C.
Downs, R.T. and Bartelmehs, K.L. (1996) Computer visualization of temperature and
pressure effects on crystal structures. EOS Transactions, AGU, Spring Meeting Supplement, 77, S261.
Downs, R.T. and Heese, P.J. (2000) Animation of crystal structure variations with pressure, temperature and composition. Reviews in Mineralogy and Geochemistry, 41,
Comparative Crystal Chemistry, Robert M. Hazen and Robert T. Downs, Editors.
Mineralogical Society of America, Washington D.C.
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software for calculating and displaying X-ray or neutron powder diffractometer patterns of crystalline materials. American Mineralogist, 78, 1104–1107.
Downs, R.T., Andalman, A., and Hudasko, M. (1996) An electron density study of the
bonding of the Na and K atoms in low albite and microcline. American Mineralogist,
81, 1344–1349.
Downs, R.T., Gibbs, G.V., and Boisen M.B. Jr. (1999) Topological analysis of the P21/c to
C2/c transition in pyroxenes as a function of temperature and pressure. EOS Transactions, AGU, Fall Meeting Supplement, 80, F1140.
Downs, R.T., Gibbs, G.V., Boisen M.B., Jr., and Rosso, K.M. (2002) A comparison of
procrystal and ab initio model representations of electron-density distributions of
minerals. Physics and Chemistry of Minerals, 29, 369–385.
Gibbs, G.V., Boisen, M.B., Jr., Hill, F.C., Tamada, O., and Downs, R.T. (1998) SiO and
GeO bonded interactions as inferred from the bond critical point properties of electron density distributions. Physics and Chemistry of Minerals, 25, 574–584.
Gibbs, G.V., Spackman, M.A., and Boisen, Jr. M.B. (1992) Bonded and promolecule
radii for molecules and crystals. American Mineralogist, 77, 741–750.
Hazen, R.M. and Downs, R.T. (1996) Systematic crystal chemistry of high-pressure silicates: An interactive graphics demonstration. International Union of Crystallography XVII Congress and General Assembly, Seattle Washington, C-543.
Hazen, R.M., Downs, R.T., and Prewitt, C.T. (2000) Principles of comparative crystal
chemistry. In Robert M. Hazen and Robert T. Downs, Eds., Comparative Crystal
Chemistry, vol. 41, p. 1–34. Reviews in Mineralogy and Geochemistry, Mineralogical Society of America, Washington, D.C.
Lipson, H. and Cochran, W. (1957) The determination of crystal structures, 345 p. G. Bell
and Sons Ltd., London.
Rakovan, J., Becker, U., and Hochella, M.F. Jr. (1999) Aspects of goethite surface
microtopography, structure, chemistry, and reactivity. American Mineralogist, 84,
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Shannon, R.D. and Prewitt, C.T. (1969) Effective ionic radii in oxides and fluorides. Acta
Crystallographica, B25, 925–945.
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MANUSCRIPT ACCEPTED JULY 26, 2002
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